Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF3793 Psest_3862 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__psRCH2:GFF3793 Length = 757 Score = 346 bits (887), Expect = 4e-99 Identities = 212/562 (37%), Positives = 319/562 (56%), Gaps = 18/562 (3%) Query: 404 IAAAPGIAIGPAHIQVLQVFDYPL----RGESCAIERERLHSALADVRRDIQGLIER--- 456 I APG +G A + VL D + ++ E +AL VR D++ L E+ Sbjct: 181 IPGAPGAGVGTALV-VLPPADLDVVPDKHIDNIDAELTLFEAALEAVRADMRNLSEKLAT 239 Query: 457 SQSKAIREIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLA 516 K R +F + MLDD L EV ++ G+ A+ A V+ ++ E + DA L Sbjct: 240 QMRKEERALFDVYLMMLDDSALGGEVTKVIRTGQWAQGALRQVVREHVRRFEMMDDAYLR 299 Query: 517 ERAADLRDIGRRVLAQL--CGVETSQEPSEPYILVMDEVGPSDVARLDPARVAGILTARG 574 ERA+D++DIGRR+L+ L +T P + ILV +E+ P+ + + ++ G+++ G Sbjct: 300 ERASDVKDIGRRLLSYLQEARQQTLTYPDKT-ILVSEELSPAMLGEVPEGKLVGMVSVLG 358 Query: 575 GATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVERD 634 + +H AI+ARA+GIP ++GA G L++DG RG + + ++ V + Sbjct: 359 SSNSHVAILARAMGIPTVMGAVDLPYSKVDGIELIVDGYRGEIITNPGKVLREQYEVLAE 418 Query: 635 TREQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAH 694 Q + R P T DGH + ++ N G A V A E+GAEG+GL RTE+ FM Sbjct: 419 QERQLSEGLDVLRELPCETIDGHRIPLWVNTGLLADVVRAQERGAEGVGLYRTEVPFMIK 478 Query: 695 PQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTL 754 + P E Q A YR L+ P+ +R+LD+GGDK LPY+PI +EENPFLG RGIR+TL Sbjct: 479 ERFPSEKEQMAIYREQLEAFHPLPVTMRSLDIGGDKCLPYFPI-KEENPFLGWRGIRVTL 537 Query: 755 QRPQIMEAQLRALLR-SADNRPLRIMFPMVGSVDEWRAARDMTERLRLEIPVADLQL--- 810 P+I Q RA+L+ SA LRI+ PM+ + E A + R E+ L + Sbjct: 538 DHPEIFLLQTRAMLKASAGLNNLRILLPMISGIGELEEALHLIHRAWCEVRDEGLDVHMP 597 Query: 811 --GIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQL 868 G+MIEVP+A L LA++VDF SVG+NDLTQY LA+DR +P ++ D LHPAVL+ Sbjct: 598 PVGVMIEVPAAVYLTRELARQVDFISVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLEA 657 Query: 869 IDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFSLSE 928 + V+ AH+ GK V +CGE+A DP A +L+ +G D LS++A ++P+VK +R+ S+ Sbjct: 658 LQRVVKEAHSEGKPVSICGEMAGDPAAAVLLLAMGFDSLSMNATNLPKVKWLLRQISMDT 717 Query: 929 AQGLAQKALAVGSPAEVRALVE 950 AQ L + + + SP +++ V+ Sbjct: 718 AQQLLARVMLLDSPQVIQSTVQ 739 Lambda K H 0.318 0.135 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1423 Number of extensions: 73 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 952 Length of database: 757 Length adjustment: 42 Effective length of query: 910 Effective length of database: 715 Effective search space: 650650 Effective search space used: 650650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory